Who We Are

Principal Investigator:

Vaughn Cooper, Ph.D

I am an evolutionary geneticist and microbiologist whose lab applies genomic technology to understand ecological and evolutionary dynamics in microbial
populations. We have pioneered methods for studying long-term evolution in biofilm populations and for measuring genome-wide mutation rates. Our focus
is pathogen evolution that occurs during chronic infections, but we also study eco-evolutionary dynamics in biofilms, the ecological context of
antimicrobial resistance, why genome regions mutate/evolve at different rates, and how the microbiome itself evolves with various conditions.
As a teacher, I advocate for the study of evolution-in-action using hands-on experiments, which we’ve developed into a simple yet powerful curriculum
for 9th-10th graders. This curriculum, called EvolvingSTEM, produces significant increases in learning of evolution and heredity, and also increases
motivation towards pursuing STEM-related careers.

My wife Erika and I enjoy spending time with our two boys and two Cardigan Welsh corgis. You’ll find often us at a swim meet, baseball diamond, soccer pitch, or when we’re lucky, fishing or vacationing at the beach or in the mountains. I still love swimming, cycling, and running (even if my knees don’t) and raced
triathlon for 25 years, including 20 Ironman finishes (7 in Kona).

Research Assistant Professor:

Chris Marshall, Ph.D

Dr. Marshall graduated from Virginia Tech in 2006 and began research in the laboratory of Dr. Harold May
in 2007 at the Medical University of South Carolina. During his Ph.D., Dr. Marshall studied anaerobic
microbial metabolism and extracellular electron transport in fermentation processes and microbial
electrochemical systems. Following completion of his Ph.D., Dr. Marshall was then awarded a prestigious
Director’s postdoctoral fellowship at Argonne National Laboratory to use computational tools to study
microbial community interactions in bioenergy production, bioremediation, and microbial ecology of wetland
systems. Dr. Marshall is currently studying the molecular targets of antimicrobial resistance and metabolic
interactions in multispecies microbial communities.

NASA Postdoctoral Fellow:

Caroline Turner, Ph.D

Dr. Turner uses experimental evolution to study ecological and evolutionary processes, particularly focusing
on the diversification of a single ancestral genotype into multiple ecologically distinct clades. She
completed her Ph.D. with Dr. Richard Lenski at Michigan State University, working with the Long-Term
Evolution Experiment with E. coli. She studied the ecological interactions between citrate-consuming
and non-citrate consuming clades which evolved and coexisted within one population of the long-term
experiment. She also studied the evolution of elemental composition in bacteria under carbon- and
nitrogen-limited conditions. As a NASA Post-doctoral Fellow in the Cooper Lab, Caroline studies the
diversification of Burkholderia cenocepacia under selection for biofilm formation and genetic patterns of
adaptation to varying environments.

Postdoctoral Associate:

Alfonso Santos-Lopez, Ph.D

Dr. Santos-Lopez has been interested in antimicrobial resistance and evolution since he started his undergrad research in 2010. He completed his Ph.D at the
Universidad Complutense de Madrid (Spain) while studying the evolution of antimicrobial resistance mediated by small ColE1 plasmids in
Pasteurellaceae. Nowadays, Dr. Santos-Lopez is studying Acinetobacter baumannii through experimental evolution, specifically focusing on how the growth mode of bacteria –biofilm vs. planktonic- affects
the emergence of antimicrobial resistance.

Postdoctoral Associate:

Eisha Mhatre, Ph.D

Dr. Mhatre completed her Ph.D at the
Friedrich Schiller University of Jena in Germany, under the direction of
Dr. Ákos T. Kovács. During her time as a Ph.D student, Eisha studied
the extrinsic factors such as environment and intrinsic factors
like growth that govern biofilm formation in Bacillus subtilis.
Currently, Dr. Mhatre is interested in studying the dynamics of multispecies
interactions in bacterial biofilms. More specifically, Dr. Mhatre wants to know how these interactions
influence the development of antibiotic resistance. She plans to use experimental evolution, population
genomics and microscopic imaging techniques to study the intricacies
of poly-microbial biofilms.

Ph.D Candidate:

Katrina Harris, B.Sc

Katrina received her bachelors in microbiology from The University of Maine in 2015 where she fell in love with microbes through studying
the mycobacteriophage ChipMunk, which she discovered her freshman year. Katrina is a PhD candidate in the Integrative Systems Biology
(ISB) program. Currently, Katrina is diving head first into the evolution world by studying the evolution of Pseudomonas aeruginosa with a
particular interest in why high mutation rates are favored in structured environments over non-structured environments.

Ph.D Student:

Michelle Scribner, B.Sc

Michelle received a Bachelor of Science in Biology from Alma College in 2016. She was first introduced to microbiology
while investigating the impact of local agriculture on the density of Escherichia coli in streams near Alma, Michigan.
She is now a Ph.D. student in Pitt’s Microbiology and Immunology program (PMI). She is particularly interested in the
evolution of Pseudomonas aeruginosa during chronic infection in patients with Cystic Fibrosis

Senior Research Specialist:

Dan Snyder, M.Sc

After receiving his bachelor degree from the University of Minnesota and Masters from Syracuse University,
Dan joined the Cooper Lab to lead the bacterial genome sequencing project that has now become MESH. The success of
MESH has led him to focus on developing automation and higher throughput techniques to allow him time to follow his
research interests in bacterial regulatory networks. Dan’s current projects involve the study of the connection between
extracellular and intracellular signal molecules in Burkholderia cepacia and the effect of evolutionarily relevant mutations on
the connection between those signals and cell lifestyle.

Research Technician:

Emily Sileo, B.Sc

Emily received her bachelors in molecular biology from Penn State University in 2016. In her studies at Penn State, Emily worked to
engineer a biodetoxification pathway for lignocellulose biomass feedstock for the iGEM 2014 competition. She grew fond of working
towards big picture ideas with microbes. Currently, Emily studies the effects on fitness and biofilm production in Burkholderia
cepacia clones as well as serving as an outreach coordinator for EvolvingSTEM. Emily hopes to continue studying the benefits of microbial
evolution and STEM education in the public health field.

Bioinformatics Research Assistant:

Nathan Phillips, B.Sc

Nathan received his Bachelors in Mathematical Biology from the University of Pittsburgh. He began working under Dr. Cooper as an
undergraduate researcher in 2015, focusing on clinical variant calling. Upon graduation, Nathan has transitioned into a full-time
role becoming the lab’s bioinformatics research assistant. He hopes to continue his work while helping both himself and others
harness the power of HPC to help solve complex computational biology problems.

Undergraduate Researcher:

Abraham Cullom

Abraham studies Civil and Environmental Engineering here at The University of Pittsburgh. In the lab, he focuses on developing new
experimental methods to examine the evolutionary ecology of opportunistic pathogens. He is also evaluating
the factors influencing the coexistence of two such bacteria: Burkholderia cenocepacia and Pseudomonas
aeruginosa. Recently, he has begun using bioinformatics to analyze the evolutionary trajectories in these
and other systems.